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- PDB-3uyu: Structural basis for the antifreeze activity of an ice-binding pr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3uyu | ||||||
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Title | Structural basis for the antifreeze activity of an ice-binding protein (LeIBP) from Arctic yeast | ||||||
![]() | Antifreeze protein | ||||||
![]() | ANTIFREEZE PROTEIN / right-handed beta-helix fold / ICE BINDING PROTEIN | ||||||
Function / homology | ice binding / Ice-binding protein / Ice-binding-like / extracellular region / Ice-binding protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, J.H. / Park, A.K. / Do, H. / Park, K.S. / Moh, S.H. / Chi, Y.M. / Kim, H.J. | ||||||
![]() | ![]() Title: Structural basis for the antifreeze activity of an ice-binding protein from an Arctic yeast. Authors: Lee, J.H. / Park, A.K. / Do, H. / Park, K.S. / Moh, S.H. / Chi, Y.M. / Kim, H.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.9 KB | Display | ![]() |
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PDB format | ![]() | 83.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.3 KB | Display | ![]() |
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Full document | ![]() | 459.4 KB | Display | |
Data in XML | ![]() | 24.4 KB | Display | |
Data in CIF | ![]() | 36.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25068.494 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 21-261 / Mutation: L86M, L172M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.4 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1M sodium acetate, pH 4.5, 1.2M ammonium sulfate, 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 29, 2011 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98227 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→36 Å / Num. all: 71952 / Num. obs: 71520 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.57→1.66 Å / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.605 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→31.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.574→1.615 Å / Total num. of bins used: 20
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